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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module _moltk'</h1><p class="nomargin-top"></p>
<p>Do not directly use the submodule &quot;moltk._moltk&quot;.  Use 
  module &quot;moltk&quot; instead. The _moltk module provides tools for 
  protein sequence/structure alignment and visualization.</p>
  <p>This submodule &quot;moltk._moltk&quot; represents the binary 
  extension implemented in C++.  The top level module &quot;moltk&quot; 
  contains all of the symbols from &quot;moltk._moltk&quot;, so use 
  &quot;import moltk&quot; of &quot;from moltk import 
  &lt;whatever&gt;&quot; to get symbols from &quot;moltk._moltk&quot;.</p>
  <p>All MolTK code is Copyright (C) 2011  Christopher M. Bruns</p>
  <p>This program is free software; you can redistribute it and/or modify 
  it under the terms of the GNU General Public License as published by the 
  Free Software Foundation; either version 2 of the License, or (at your 
  option) any later version.</p>
  <p>This program is distributed in the hope that it will be useful, but 
  WITHOUT ANY WARRANTY; without even the implied warranty of 
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
  Public License for more details.</p>
  <p>You should have received a copy of the GNU General Public License 
  along with this program; if not, write to the Free Software Foundation, 
  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</p>
  <p>Commercial users should ask about our dual licensing model. For 
  questions contact: cmbruns@rotatingpenguin.com</p>

<!-- ==================== CLASSES ==================== -->
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Aligner-class.html" class="summary-name">Aligner</a><br />
      The Aligner class creates macromolecule sequence alignments and 
        structure alignments.
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Alignment-class.html" class="summary-name">Alignment</a><br />
      Alignment represents a set of aligned macromolecule sequences 
        and/or structures.
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Angle-class.html" class="summary-name">Angle</a><br />
      Quantity represents a physical value with a unit, such as 5.6 nanometers
    </td>
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.AngleDimension-class.html" class="summary-name">AngleDimension</a><br />
      Dimension represents a physical dimension such as mass, length, 
        time, etc.
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.BaseBiosequence-class.html" class="summary-name">BaseBiosequence</a><br />
      Parent class for macromolecule sequences and structures.
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.Biosequence-class.html" class="summary-name">Biosequence</a><br />
      A macromolecule sequence (DNA or RNA or protein)
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.BiosequenceResidue-class.html" class="summary-name">BiosequenceResidue</a><br />
      One residue in a macromolecule sequence (a nucleotide or amino 
        acid)
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.BitUnit-class.html" class="summary-name">BitUnit</a><br />
      Unit represents a unit of measure, such as gram, nanometer, or 
        second.
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.DimensionIndex-class.html" class="summary-name">DimensionIndex</a>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Displacement-class.html" class="summary-name">Displacement</a><br />
      Vector3D_&lt;&gt; is an arbitrary point or vector in 3-space.
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.EString-class.html" class="summary-name">EString</a><br />
      A compact representation of the gapping pattern for one sequence in
        an alignment.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Information-class.html" class="summary-name">Information</a><br />
      Quantity represents a physical value with a unit, such as 5.6 nanometers
    </td>
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.InformationDimension-class.html" class="summary-name">InformationDimension</a><br />
      Dimension represents a physical dimension such as mass, length, 
        time, etc.
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.Length-class.html" class="summary-name">Length</a><br />
      Quantity represents a physical value with a unit, such as 5.6 nanometers
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.LengthDimension-class.html" class="summary-name">LengthDimension</a><br />
      Dimension represents a physical dimension such as mass, length, 
        time, etc.
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.NanometerUnit-class.html" class="summary-name">NanometerUnit</a><br />
      Unit represents a unit of measure, such as gram, nanometer, or 
        second.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.PDBStructure-class.html" class="summary-name">PDBStructure</a><br />
      PDBStructure represents a macromolecule structure as found in a 
        Protein Data Bank file.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Printable-class.html" class="summary-name">Printable</a><br />
      moltk::Printable is an abstract base class to help streamline 
        string conversion in the moltk python bindings.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Quaternion-class.html" class="summary-name">Quaternion</a><br />
      Quaternion is an elegant 4-element representation of a 3D rotation.
    </td>
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.QueryPositionList-class.html" class="summary-name">QueryPositionList</a>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.RadianUnit-class.html" class="summary-name">RadianUnit</a><br />
      Unit represents a unit of measure, such as gram, nanometer, or 
        second.
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.RigidTransform-class.html" class="summary-name">RigidTransform</a><br />
      RigidTransform converts one reference frame to another with 
        rotation and translation.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Rotation3D-class.html" class="summary-name">Rotation3D</a><br />
      Rotation3D represents a rotation matrix.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.UnitVector3D-class.html" class="summary-name">UnitVector3D</a><br />
      UnitVector3D represents a direction in 3 space, and, unlike 
        Vector3D_&lt;&gt;, does NOT have Units.
    </td>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk.Vector3D-class.html" class="summary-name">Vector3D</a><br />
      Vector3D_&lt;&gt; is an arbitrary point or vector in 3-space.
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      <span class="summary-type">&nbsp;</span>
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        <a href="moltk.std_vector_int-class.html" class="summary-name">std_vector_int</a>
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<!-- ==================== FUNCTIONS ==================== -->
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          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#align" class="summary-sig-name">align</a>(<span class="summary-sig-arg">...</span>)</span><br />
      align( (Alignment)target_alignment, (Alignment)query_alignment) -&gt; Alignment :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
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        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#cos" class="summary-sig-name">cos</a>(<span class="summary-sig-arg">...</span>)</span><br />
      cos( (Angle)angle) -&gt; float :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#get_unit_name" class="summary-sig-name">get_unit_name</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_unit_name( (RadianUnit)arg0) -&gt; str :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#get_unit_symbol" class="summary-sig-name">get_unit_symbol</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_unit_symbol( (RadianUnit)arg0) -&gt; str :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#load_fasta" class="summary-sig-name">load_fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      load_fasta( (str)file_name) -&gt; Alignment :
     global load_fasta method helps get SEQUOIA-like conciseness in python.</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk%27-module.html#sin" class="summary-sig-name">sin</a>(<span class="summary-sig-arg">...</span>)</span><br />
      sin( (Angle)angle) -&gt; float :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
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         ><span class="options">[<a href="#section-Variables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
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  </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_AMOUNT"></a><span class="summary-name">DIMENSION_AMOUNT</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_AMOUNT">moltk._moltk.DimensionIndex.DIMENSION_AMOUNT</code>
    </td>
  </tr>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_ANGLE"></a><span class="summary-name">DIMENSION_ANGLE</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_ANGLE">moltk._moltk.DimensionIndex.DIMENSION_ANGLE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_CHARGE"></a><span class="summary-name">DIMENSION_CHARGE</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_CHARGE">moltk._moltk.DimensionIndex.DIMENSION_CHARGE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk%27-module.html#DIMENSION_INFORMATION" class="summary-name">DIMENSION_INFORMATION</a> = <code title="moltk._moltk.DimensionIndex.DIMENSION_INFORMATION">moltk._moltk.DimensionIndex.DIMENSION_<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_LENGTH"></a><span class="summary-name">DIMENSION_LENGTH</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_LENGTH">moltk._moltk.DimensionIndex.DIMENSION_LENGTH</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_MASS"></a><span class="summary-name">DIMENSION_MASS</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_MASS">moltk._moltk.DimensionIndex.DIMENSION_MASS</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="DIMENSION_TIME"></a><span class="summary-name">DIMENSION_TIME</span> = <code title="moltk._moltk.DimensionIndex.DIMENSION_TIME">moltk._moltk.DimensionIndex.DIMENSION_TIME</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="__package__"></a><span class="summary-name">__package__</span> = <code title="None">None</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="bit"></a><span class="summary-name">bit</span> = <code title="&lt;moltk._moltk.BitUnit object at 0x0249A260&gt;">&lt;moltk._moltk.BitUnit object at 0x0249A260&gt;</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="nanometer"></a><span class="summary-name">nanometer</span> = <code title="&lt;moltk._moltk.NanometerUnit object at 0x0249A298&gt;">&lt;moltk._moltk.NanometerUnit object at 0x0249A298&gt;</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="radian"></a><span class="summary-name">radian</span> = <code title="&lt;moltk._moltk.RadianUnit object at 0x0249A2D0&gt;">&lt;moltk._moltk.RadianUnit object at 0x0249A2D0&gt;</code>
    </td>
  </tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Function Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-FunctionDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
</table>
<a name="align"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">align</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

align( (Alignment)target_alignment, (Alignment)query_alignment) -&gt; Alignment :

    C++ signature :
        class moltk::Alignment align(class moltk::Alignment,class moltk::Alignment)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="cos"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">cos</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

cos( (Angle)angle) -&gt; float :

    C++ signature :
        double cos(struct moltk::units::Quantity&lt;struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,1,0&gt; &gt;,double&gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_unit_name"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_unit_name</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_unit_name( (RadianUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_name(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,1,0&gt; &gt;)

get_unit_name( (NanometerUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_name(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,1,0,0,0,0,0&gt; &gt;)

get_unit_name( (BitUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_name(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,0,1&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_unit_symbol"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_unit_symbol</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_unit_symbol( (RadianUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_symbol(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,1,0&gt; &gt;)

get_unit_symbol( (NanometerUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_symbol(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,1,0,0,0,0,0&gt; &gt;)

get_unit_symbol( (BitUnit)arg0) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_unit_symbol(struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,0,1&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="load_fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">load_fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

load_fasta( (str)file_name) -&gt; Alignment :
     global load_fasta method helps get SEQUOIA-like conciseness in python.

    C++ signature :
        class moltk::Alignment load_fasta(class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="sin"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">sin</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

sin( (Angle)angle) -&gt; float :

    C++ signature :
        double sin(struct moltk::units::Quantity&lt;struct moltk::units::Unit&lt;struct moltk::units::Dimension&lt;0,0,0,0,0,1,0&gt; &gt;,double&gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
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  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
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        <td align="left"><span class="table-header">Variables Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-VariablesDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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<a name="DIMENSION_INFORMATION"></a>
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  <h3 class="epydoc">DIMENSION_INFORMATION</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
moltk._moltk.DimensionIndex.DIMENSION_INFORMATION
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